ABSTRACT Increasing evidence suggests that autoantibodies antecede overt clinical disease by years, inclusive of anti- SSA/Ro among the earliest reactivities. Predicting who will progress would be a critical translational discovery. Mothers in the Research Registry for Neonatal Lupus (RRNL) represent a unique population at risk for overt clinical autoimmunity. Despite high titer anti-Ro antibodies pathogenic to the developing fetus, many women are asymptomatic and autoimmunity is identified solely based on disease in their offspring. In the RRNL, 243 of 500 mothers were asymptomatic or had minimal symptoms at the birth of the NL child. Nearly half of these mothers later developed systemic lupus erythematosus (SLE) and/or Sjgren's syndrome (SS). The identification of numerous susceptibility genes disproves a purely environmental cause for autoimmune diseases such as SLE, but susceptibility genes are not sufficient for the development of disease. In fact, the disease probability given the genotype remains modest. These observations strongly imply that gene- environment interactions contribute to the risk of SLE. One environmental factor is an individual's microbiome, given the constant interchange between the immune system and bacterial species whose products prime cells within the innate and adaptive immune systems. We hypothesize that some HLA variation drives a pathologic microbiome which associates with progression from benign to pathologic autoimmunity and overt clinical disease. In addition, other HLA variation may correlate with a protective microbiome and clinical quiescence. In Aim 1, associations will be sought between host genetics and anti-Ro NL maternal disease status. Feasibility of the approach is based on prior genotyping of 147 RRNL mothers using the Illumina Immunochip. From Immunochip SNPs, classical 4-digit HLA alleles have been imputed yielding a total of 119 unique HLA alleles. It will be determined whether SLE risk alleles, identified by the SLE Immunochip Consortium, correlate with maternal disease status, and whether the SLE genetic risk allele load correlates with material disease status. In Aim 2, we will test for associations between gut bacterial species in the context of HLA and anti-Ro NL maternal disease status. Using a DNAseq library from amplification of 16S rRNA gene regions, non-adjusted for maternal HLA, preliminary results of microbiota profiling revealed an abundance of protective Rikenellaceae and Oscillospira in 8 asymptomatic anti-Ro+ NL mothers compared to 35 overt SLE patients. Overall abundance, microbial diversity, and specific operational taxonomic units (OTUs) will be correlated with HLA variation, specific SLE/SS-risk variants, and overall SLE risk allele genetic load. In Aim 3, stool samples will be collected from mothers enrolled in the RRNL who have been previously genotyped but in whom matched samples have not yet been provided. To our knowledge, the proposed experiments will be the first to characterize the impact of a patient's microbiota on a preclinical disease state and to test whether host genetic variation at the MHC locus influences a pathologic microbiome.